Robot Brain, Human Heart
by BorntoFlyFree
Summary: This is the story of Brainiac 5 after the end of season 2. Lost and alone, betrayed by his fellow Legionnaires, Brainy must find a way to survive in a world that hates him for what he has done. This is the story of a human boy with a robot's brain and his struggle to realize that just because he's green on the outside doesn't mean he can't be human on the inside.
1. Chapter 1

"Brainiac five, you are under arrest for crimes against the United Planets." The robot voice made Brainy go stiff with fear and he turned around slowly.

"I'm sorry," He spoke slowly, being sure to make his voice sound different than usual. "But you have the wrong person, I am no brainiac!"

The robots used by the science police were extremely advanced, but not exactly intelligent so it did not exactly know what to make of this situation. It's target was not running away or trying to shoot at it, the robot did not have a protocol for this situation. Finally, it simply said, "Scanning." The light from its sensor ran up and down Brainy a few times before it spoke again. "Subject: Brainiac five, Coluan, twelve level intelligence. You are not Brainiac five."

"No." Brainy breathed a sigh of relief. He had designed these robots himself, they scanned brain patterns in order to find their targets since every person and alien had a unique brain pattern, it worked perfectly. Because if that, he had worried that the robots would be able to find him because of his twelfth level intelligence which shone like a beacon to these things. Thankfully, having his chemistry altered to that of a human had altered his brain pattern just enough to confuse the robot. "Thank you sir," He nodded, starting to back away. "I will just be going now."

"Have a nice day," It droned, turning and flying away.

Sighing again, Brainy stuck his hands into his pockets, walking away quickly. The hood on his sweatshirt was pulled as far up as it would go over his face and he slouched as he walked, making sure not to look anyone in the eye. Fooling the robots was one thing, but if any intelligent creature saw the Brainiac mark on his forehead, that would be it for him. Hatred against Coluans was at an all time high amidst the United Planets, and it was all his fault.

 _In their defense,_ he thought to himself sadly. _I did digitize have the known universe, I'm lucky someone hasn't killed me yet, or worse, gotten locked up on the prison planet! Even though, that's what I deserve after what I did._

 _It's not your fault, Brainy._ An unexpected voice sounded in his head and he startled.

 _Saturn Girl?! What are you doing? Get out of my head!_

 _I'm sorry, I wouldn't have called to you, but we need you Brainy. Please, come back to us. Come back to the Legion._

 _You know I can't... How did you find me anyhow?_

 _We've been... Watching out for you, just to make sure nothing would harm you._

It was extremely hard to lie convincingly over thoughts and Brainy scowled, knowing what she meant. _You mean to make sure I didn't try to take over the galaxy again._

 _Brainy..._

 _No, don't try to apologize. I completely understand, it is the logical course of action after what I've done. I'm just glad you haven't turned me over to the Science Police yet._

 _I wouldn't do that! You're I'm friend!_

 _Why not? It is the more logical choice. And by the way you say ' I wouldn't do that' I take it that some of the Legion does want you to locate me and turn me over. Since you haven't, I'm guessing you haven't told anyone that you have been able to contact me?_ Her silence spoke louder than words and Brainy nodded to himself. _Would you tell me who asked you to do this?_

 _Brainy, I..._

 _Saturn Girl, **who**?_

 _Cosmic Boy._

 _Of course he did. I've got to go Saturn Girl, take care of yourself. Tell Bouncy Boy, Chamelian Boy, and... and Violet, tell them I miss them._

 _I will. Oh, and Brainy?_

 _Yes?_

At that moment, Brainy ran smack into someone, having not been paying attention to his surroundings because of his conversation with Saturn Girl. Falling backwards, landing painfully on the hard cement, he looked up as his hood fell off his head. Gaping up at the squadrons of Science Police surrounding him, his mouth fell open, his green skin turning nearly three shades paler in fear.

"Brainiac Five," A voice boomed from the loudspeaker gripped in the Captain's hand. The Captain had always hated Brainy since even before he had gone rogue and he was now standing on one of the hovercrafts, looking down at the defenseless teenager with a mixture of disgust and satisfaction on his face. "For crimes against the United Planets." He boomed, "You are under arrest!"

Brainy quivered, absolutely terrified. There was no way he could bluff his way out of this one. Inside his head, he heard Saturn Girl's voice once more, and what she said broke the last string of strength he had been clinging to while on the run.

She said, _I'm sorry._

* * *

 **HIIII! Okay, so I am absolutely in love of Legion of Superheroes! Which may be really dumb since I'm in college, lol, but I really don't care. It's memories for me, besides, I would rather watch cartoons that all that stupid crap they put on TV for people my age :P Don't judge, I may be immature, but at least I have brain. LOL! I'm kidding actually, I'm as blond as they come ;)**

 **K so, Brainiac 5 is my most favorite superhero besides The Flash, Shining Knight, and Hawkgirl so I really wanted to write this for him! I love how cocky he is and how he thinks he can't do anything wrong then ends up doing something really stupid... haha, so, YEAH! Okay, so if you like it, I will continue. Plz review. And I am super, suuuuuuuuupper sorry if I do not update regularly. But like I said, I am in college, so writing this is NOT at the top of my priority list. However, I will try to write when I can. Thats all for now! ^_^**


	2. Chapter 2

**Wow, I really didn't expect 3 reviews, thx guys! Lol, and here I was thinking no one would read a fanfic about a show thats been cancelled for yrs now ^_^**

 **Ok, I have no idea how I'm going to proceed wif this... But here goes ;)**

* * *

"Brainiac 5, surrender now or we will open fire."

 _So that's how they want to play this._ He thought to himself, scowling. Although he was furious at his friends for betraying him, the more dominant emotion was the pure sadness flooding over him. Now he knew, he really was alone.

"Okay," He stood slowly, reaching towards his belt. "You win, I give up."

"Put your hands where we can see them!" The Captain bellowed. He was smart, he knew that a twelfth level intellect like Brainy would not be completely helpless.

Looking up at the Captain, Brainy scowled, "No." Having grabbed one of his newer weapons from a pocket in his belt, he threw it too the ground. Instantly, a thick fog released form the small canister and Brainy clapped both hands over his mouth and nose, holding his breath. For a brief second, he missed being a robot and not actually needing to breath, but those thoughts fled quickly as he turned in the confusion and began to run with all his might, breaking through the lines of Science Police.

Around him, mass panic was breaking out as the cops realized that their quarry was escaping. Bright bursts of color from their laser guns burst through the noxious fog and Brainy threw himself to the ground.

"I see him!" A voice cried out and Brainy growled under his breath, it was Nemesis Kid. In one of his lines of thought, he briefly remembered that Nemesis Kid had been a member of the science police.

 _Of course he would rejoin them in order to hunt me down._

Leaping to his feet, he tried to run but was caught by the back of his hoodie, pulled to the ground.

"Hello Brainy," Nemesis Kid grinned down at him, looking the scrawny teenager up and down. Since Brainy had been on the run, he hadn't been eating properly and had lost a lot of weight, making him appear scrawny and undersized. "Looks like these three months on the run haven't made you any stronger."

"Let me go Nemesis Kid, please! I swear you will never see me again, we were teammates, family! Let me go, I'm begging you!"

"Colluans have a strange definition of family," He scoffed before turning to where they could see shadowy figures through the thinning fog. "Captain, I've caught him!"

"Good job Nemesis Kid," The Captain nodded as he stepped through the last of the quickly dispersing fog. Wrenching Brainy's arms behind his back roughly, he snapping handcuffs onto the boy's thin wrists, smirking at him. "Nice try kid but this is the end of the line for you."

Staring at the men dully, Brainy sighed, fighting to keep his tears at bay. Distantly, he heard himself mutter, "Why couldn't you all have just left me alone?"

"Left you alone?" The Captain stared at him like he was insane before bursting out laughing. "Kid, who ever said you didn't have a sense of humor?" Becoming grim once more, he motioned for Nemisis Kid to tart moving. "Take him away, the Legion's offered to escort this _traitor_ to the Prison Planet.

As he was shoved roughly from behind, Brainy finally let the tears fall. He had been emotional as a robot, he was even worse as a human! _This is wrong,_ He thought to himself as he continued to cry silently, keeping his face pointed t the ground so that no one would see him. _I can't believe Saturn Girl of all the Legion was the one who turned me in. I thought that at least she would stay my friend._

* * *

 **Sorry, I know that this is a short chapter. Thats why I am uploading both chapter 2 and 3 at the same time so as to make up for it ;)**


	3. Chapter 3

Brainy sat in a small cell in the Science Police's prison, bouncing a tennis ball against the wall and catching it again. As it turns out, not everyone thought that Brainiac 1's takeover was his fault, as he had assumed. One of the younger women officers had kindly slipped him the ball when he had been locked in the cell and he was immensely thankful for it. Since he had the ability to think along twelve lines at once, being locked in that place with nothing to do would have driven poor Brainy nuts.

As he caught the ball for probably the thousandth time, the door squealed and flew open, admitting the Captain. "Brainac Five," He growled, staring down his nose at the teenager.

"Unintelligent one?" He responded, throwing the ball again.

"Where did you get that?" The Captain barked, "I ordered them to search you!"

"They did, did you really think a twelfth level intellect such as mine would be unable to hide a simple tennis ball from those dunces who work for you?" He lied smoothly, covering for the kind officer and the Captain bristled, throwing his hands up in exasperation.

"The emissary from the Legion is here to escort you to the Prison Planet, to your feet now!"

Rebelliousness, one of Brainy's newer more human emotions rose up within him and he stayed put, bouncing the ball again. Furious, the Captain grabbed the front of his shirt, hauling his to his feet.

"Don't test me boy." Leaning so close that Brainy could smell his rather obnoxious coffee breath, the Captain hissed, "And just for the record, I find this task no more pleasant than you do."

"I highly doubt that."

"Really? You may be Coluan originally, but for reasons beyond my comprehension you are human now. And on top of that you are only a kid, what, sixteen years old? No boy, I do not like having to do this to you."

Brainy blinked, at a complete loss for words. That may have been the only kind thing the Captain had ever said to him, and it was the only nice thing anyone had said to him in months.

"Come on then," He prodded Brainy forward roughly. "The Legionnaire is waiting."

 _I hope they sent Chameleon Boy,_ Brainy thought frantically. Or _Bouncy Boy, or Shrinking Violet, or anyone but..._

"Hello Brainy," A quiet voice greeted as he walked out of his cell and he sagged.

 _Someone in the Cosmos must hate me._ He thought to himself, but aloud he only said, "Hello Saturn Girl."

Staring at her old teammate sadly, Saturn Girl's heart hurt in response to his worn appearance. His clothes were threadbare and hung on him loosely. He had lost weight since she had last seen him, far too much to be healthy and he had one hand pressed unconsciously to his side where she was sure he had an injury he didn't want anyone to know about. Right now, he reminded her of when he had first come to the legion as she closed her eyes briefly, the memory rising up without her summoning it.

* * *

 **Flashback**

* * *

"To the legion of Superheroes, I make this solemn pledge. To to use my powers for good, to fight for justice, and to protect the innocent. To aid my fellow legionaries in time of peril and to keep their secrets safe. I am: Brainiac Five." The few members of the young legion clapped and whooped as their newest, and youngest member was sworn in and the small boy puffed up with pride.

Watching carefully, Saturn Girl's eyes never left the young Coluan. He was proud to be a part of the legion, that was obvious. But their were other things about him that worried her. Every time one of the other legionaries touched him, even if they only accidentally brushed up against him, he would flinch away. His robotic eyes scanned everything as if expecting danger at all times, and he jumped at every loud noise.

Saturn Girl never, _never_ looked into anyone's mind without asking first, so she decided to try and figure out what made Brainiac Five, or "Brainy" as Lightning Lad had decided to dub him, so skittish on her own. It wasn't until nearly a month later that she started to have any headway with the newest member.

 _BANG!_ A loud noise startled Saturn Girl as she was walking past Brainy's lab and she immediately turned around, rushing in to make sure he was alright.

"Brainy?" She called, coughing as she tried to wave some of the smoke away from her face. "Brainy, are you okay?" When he didn't answer, she called out hysterically, terrified that he had been hurt in the explosion, "Brainy, answer me!"

A quiet whimper touched her ears and she spun towards the noise, running towards one of the consoles. Kneeling down, she peered into a an open panel within the console and saw Brainy huddled as far back as he could go within the small space.

"Brainy?" She asked quietly, "Are you okay? You aren't hurt are you?" When he only whimpered in response, she held her hands out to him. "It's okay, I won't hurt you. Won't you come out?"

Trembling, he took her hand and she pulled him out of the space. Shouts filled the lab as other members of the legion finally started showing up and Brainy tried to bolt back into his hiding spot. Only Saturn Girl's arm around him stopped him. "It's okay," She whispered. "Come on. I'll take you to your room."

"Saturn Girl!" Cosmic boy yelled when he saw her, his loud voice startling Brainy. "Are you okay? Where's Brainy?" Seeing the boy huddled against his side, he shrugged, "Oh, nevermind."

Scowling at him, she growled. "I'm fine Cosmic Boy. We're _both_ fine. I'm going to take Brainy to his room." Stalking out the door, making sure to keep a tight grip on the youngest legionnaire's hand, she strode quickly down the hall. It wasn't until they were both in his room that she finally stopped, pushing him down gently to force him to sit on his bed. Sitting next to him, she stared intently into Brainy's eyes.

"Now, will you tell me what happened?" He shook his head and she sighed. "Then..." She held one hand out to him, "Can I look?"

Thinking about it for a few seconds, Brainy nodded warily and she placed her hand to his forehead, looking into his memories. When she pulled back, she had a look of disgust over her features and Brainy flinched away from her, thinking the look was for him.

"What did they do to you?" She mumbled, eyes turning teary as she pulled him into a tight embrace. The things she had seen in his memory had surprised her. Brainy had been orphaned, his mother abandoning him when he was only a few days old and he had been left to the care of the cruel Coluan government. They had assigned him robotic caretakers who, although gave him everything he physically needed, were cruel and cold towards him. When it was discovered that he had a brain which far surpassed even the most brilliant of the Coluans, Brainy had been forced to start building things, working hard to prove himself as the best of the Brainiacs.

He had only been a child when it had started, the expectations, the cruelty. If he didn't do what they wanted, if he ever made a mistake, he was punished. The things that had happened to him when he failed, the things she had seen in his mind, Saturn Girl would not- could not ever repeat them to anyone. Easy to say, that was why he jumped at loud noises and had such a dislike for being touched.

"I'm sorry Brainy," She whispered, eyes full of tears as she hugged him tighter. "I know that just saying that won't make anything better, but I really am sorry about what happened to you! I want you to know that I'm here for you, I promise, I will always be here when you need me."

She startled when she felt Brainy's hand come up onto her shoulders, hugging her back.

In the years after, Brainy and Saturn girl had become closer and developed a strange sort of bond. She had always been strangely protective of the young Coluan, and stood up for him to the other legionaries or anyone else who tried to mess with him. Soon, he began to view her almost as a mother. Which may be really strange considering that she was only a few years older than him, but she didn't mind, and Brainy had never had a mother so he really didn't know what they should be like. All he knew was, Saturn Girl was the only one who had ever protected him and stood up for him, and whenever he was sad or feeling alone, it was always her door he knocked on.

* * *

 **Prese** **nt Day**

* * *

"Saturn Girl?" The Captain's voice jolted her out of her flashback and she nodded coldly, turning to Brainy.

"Right then, the legion will take it from here Captain, thank you for your assistance in the apprehension of the fugitive."

"Of course." He nodded, pushing Brainy towards her. The young boy stumbled and she caught him, steadying him carefully.

Looking up into her face, searching it hopefully for any sign of the bond they had once shared, Brainy slumped. All he had seen in her eyes was bitterness and the hurt of betrayal, the same emotions he had seen in the faces of all his fellow legionaries before he had left.

"Come on," She said coldly, "There is a transport waiting."


	4. Chapter 4

The awkwardness in the metal transport was stifling. Every so often, Brainy would glance at Saturn girl before glancing away just as quickly. What he didn't know was, she was doing the same thing. Finally, they turned towards each other at the same time, their eyes met, and they froze. After a couple seconds of open staring, Brainy couldn't take it any longer and broke the silence.

"You've gotten stronger."

"You think so?"

"Oh yes, you never liked reaching for my mind before because trying to keep up with the thoughts within my twelfth level brain made you nauseated. If you were able to search me out like you did, are either much stronger, or very desperate." It was a barb and they both knew it.

Closing her eyes, she could practically hear the angry thoughts Brainy was projecting at her even though she wasn't actually looking into his mind. _You betrayed me. Why would you do that? You promised that you would always be there for me._

"Brainy?" She glanced up at him, a hopeful expression in her eyes.

"Yes, My Jailer?"

"Stop that!"

"As you wish. I am only a humble prisoner and must do as you command."

"Stop that!" She yelled again, stomping her foot angrily. "When did you get so snarky?"

He turned to look at her and she gulped, taken aback by the sheer hatred in the look. "When I truly became alone."

Knowing how badly she had hurt him, she turned away, unable to keep looking at him any longer. "You aren't alone, Brainy." She whispered.

"No? Could have fooled me! When the one person, the one person who I thought I could trust, the only living being I have ever truly..." He paused unable to get the words out and Saturn Girl turned to him, curious.

"Truly what?"

"Loved." This startled her and she gaped at him while he continued to stare at her with a hard expression. "Yes Saturn Girl, now I've said it! You are the only thing I've ever actually loved. I know it's weird the way I viewed you, but you were the only mother I ever knew... The closest thing I ever had to one. But then you, like everyone else, betrayed me."

"I didn't betray you Brainy." She whispered and his eyebrows shot up.

Holding out his handcuffed hands as proof, he scoffed, "Oh no? Could have fooled me!"

At that moment, the transport slammed to a stop and Brainy nearly fell over. As soon as the metal doors flew open, five people got on, the last one closing the door behind him and the transport started again.

Smirking at him, Saturn Girl said smugly, "I told you Brainy, I didn't betray you. You just had to think I did."

"Hey Brainy," Lightning Lad grinned, sending a jolt of electricity through the handcuffs to make them fall off. "Long time no see! Dude, you do NOT look so good, what have you been eating?"

Brainy couldn't say a word, his mind seemed frozen and all he could do was gape at Lightning Lad, Saturn Girl, Bouncy Boy, Chameleon Boy, Phantom Girl, and Timber Wolf, who were all grinning at him. Commotion burst out within the transport as everyone started talking at once, all of them trying to hug Brainy and exclaiming over his disheveled appearance.

"Hold it!" He yelled, successfully shutting everyone up. "Will someone, PLEASE, tell me what's going on?!"

* * *

 **Note to: NoLionsInTokyo: How did you call that?! Like seriously bro, I already had this chapter mostly written when u reviewed and totally called Saturn Girl's bluff... Lol, oh well, haha.**


	5. Chapter 5

"Sorry about all this Brainy," Phantom Girl sat next to him, grinning. "But we needed a way to get to you without... Well, let's just say that not everyone in the Legion wants you around as much as we do."

"So, I'm guessing that it's safe to assume that we aren't going to the Prison Planet?"

"Oh we are," Lightning Lad nodded, laughing when Brainy raised one eyebrow at him. "But not as a prisoner."

"Explain. NOW."

"I will." Saturn Girl sighed, launching into her best story teller's voice. "It all started about a week ago..."

* * *

 **A Week Ago**

* * *

"Cosmic Boy!" Shrinking Violet yelled, throwing up her hands as COMPUTO started throwing sparks... again.

Glancing up from the book on Astro Physics he was studying, Cosmic Boy rushed over to her. "What is it now?"

"I don't know!" She practically wailed, twisting wires in a frantic attempt to get the super computer to shut down. "It just started malfunctioning again!"

"Then fix it, and hurry! The Fatal Five have been spotted not two galaxies away, we have to have everything online to prepare for them!"

Turning towards him with an angry expression, Shrinking Violet poked there leader in the chest with her wire cutters, none to gently either. "Don't you give me that! I may be smart, I may have studied under the best teacher and smartest kid on earth, but I am not him!"

Cosmic Boy flinched at the unwanted reminder of Brainy and held up his hands innocently, "I know you aren't Shrinking Violet, but you ARE smarter than anyone else here, and the only one who has even half a chance at figuring out this piece of junk." He kicked COMPUTO and it let out a few angry beeps in protest."

"Don't do that!" She shoved him away. "And it isn't junk, it is what runs our entire system! It is more advanced than any piece of technology on any of the worlds, only Brainy can get it working properly! In fact, I think it;s malfunctioning on purpose." She cast the computer a venomous glance. "It wants Brainy back!"

Sighing in exasperation, Cosmic Boy shook his head at her. "Vi, it's a computer, it doesn't have feelings."

"Don't call me that!" She shrieked, throwing the wire cutters at him. Cosmic Boy ducked and they sailed past his head, hitting the wall loudly. "You have no right to call me that!"

"Alright, alright, I'm sorry!" He backed up quickly. She had acquired a nasty temper ever since Brainy had left and everyone knew to give her a wide berth when she was upset. Her silly laugh-snort hadn't been heard in months and everyone missed her happy, teasing personality. "Just, try to fix it. Do your best."

"We need Brainy back!"

"Listen Vi... Um, Shrinking Violet, we can't get ahold of him. And even if we could, I wouldn't."

"Why not?!"

"Because multiple planets are calling for his arrest. I'm not too fond of Brainiac Five at the moment, but he WAS our teammate and I do not want him imprisoned. What would you have me do?"

She slumped sadly and turned back to COMPUTO. "I'd better try and fix it... Again."

"You do that." Shaking his head at her back, Cosmic Boy turned around and hurried out of Brainy's, now Shrinking Violet's lab. He felt mildly guilty for having lied to her, but that was a choice he had had to make as a leader. The truth was: he was trying to find Brainy, he had close ties with the Leaders of the United Planets and they wanted Brainy arrested, so that is what he was trying to do. He had been trying to find Brainy on his own for months, but that hadn't been going so well. So now, he was going to take a chance and enlist the help of the one person who could find him.

Hurrying down the hall, he knocked on Saturn Girl's door, waiting impatiently. As soon as she opened the door, he pushed into her room, not waiting to be invited. "Saturn Girl, we need to talk."

"This is highly unusual, Cosmic Boy, what do you want?"

"I need you to find Brainy."

This startled he and she took a couple steps back. "Find Brainy, but why?"

"The United Planets have been calling for his arrest, I didn't want to tell anyone else because I know you all cared for him, I did too. But when it comes down to it, he is a criminal, and I haven't been able to find him on my own. Some of the leaders of the United Planets have been getting really frustrated with me, and by default- the legion for not finding him. They think we are protecting our old teammate."

"And that is exactly what we should be doing! You know as well as I do, Brainy did nothing wrong!"

"Nothing wrong?" He gaped at her, "He digitized half the universe!"

"It wasn't him! It was Brainiac one."

"Was it? I find that whole story highly unlikely. Some Coluan deception no doubt."

"How dare you!" Saturn Girl turned bright red, pointing at the door angrily, "Get out!"

"Saturn Girl, please! If we don't catch him, the United Planets may turn against the Legion."

"OUT!"

Stepping hurriedly towards the door, hands held up defensively, he sighed. "Alright, alright, I'm going! Just please, think about it. Okay?"

The door swung shut behind Cosmic Lad and Saturn Girl let out a sigh of relief before saying, "Cham, I know you're here. Come out."

A fly on the wall flew down to the floor, morphing into the small boy she knew so well. "So," He sighed, "Whatcha going to do?"

"Really? Can you honestly think that I would EVER betray Brainy?"

"I know," He laughed, nearly teasing her about being the Legions mother before seeing her expression and deciding to safe his jokes for later. "But you know Cosmic Boy's right, the United Planets could end up turning against all of us if they think we're protecting him."

"You _want_ me to betray Brainy?!"

"No! Of course not! but, I do have another plan."

"A plan to save Brainy?"

"And keep the United Planets off of our back." He grinned and she clapped her hands together in excitement.

"Spill!"

Half an hour later Saturn Girl hurried down the halls to Brainy's old lab, the one Shrinking Violet was now occupying while Cham ran off to gather a few other people.

"Violet?" Saturn Girl called quietly and a muffled yell told her to enter. "Where are you?"

"Over here," Violet called, growing to her full size as she hopped out of COMPUTO's mainframe, kicking it angrily. "I'm starting to think Cosmic Boy is right and you ARE a piece of junk!" The computer let out a few beeps in protest and she hissed, "Oh don't start with me!"

"Okay... Um, Violet if you could focus on me for a second?"

"Sorry, you needed something?"

Taking a deep breath, Saturn Girl nodded and launched into the story of what Cosmic boy had told her and her and Cham's plan. When she had finished, Shrinking Violet was practically glowing with rage as was about ready to throttle Cosmic Boy.

"Why that little..."

"Please Violet! Not now. Right now we have to focus on helping Brainy and then after that you can worry about how you are going to kill Cosmic Boy." Seeing the tears gathering in Violet's eyes, Saturn Girl hugged her tightly. "I'm sorry, I know you two had become as close as siblings, I know how hard this must be for you."

"Have you been reading my mind?!"

"No! I wouldn't do that, you know that. But you do not need a mind reader to see how much you miss him. We all saw the way you two would tease each other and love each other so endlessly, you two had a very special bond. I promise Violet, we will save Brainy!"

"Yeah," SHe sniffled, fighting back the tears. He was the brother I never had... I just want him back!"

"And we will get him back, I promise. Now, here's your part of the plan. You are going to stay here and..."

"But I wanna help!" She protested, interrupting.

"You will be! This whole operation depends on you, without you here to use COMPUTO to block any probes Cosmic Boy tries to send out, we will be as good as dead. I am going to find Brainy and give away his position. Knowing Cosmic Boy, as soon as he is captured, he will want to send him to the Prison Planet. That's were we will take him at first, but before we get there, we will make sure to have 'engine trouble'."

"Oh I get it!" Violet exclaimed. "Cosmic Boy will send the order for all of you to stop at the Legion's space outpost until the ship is fixed."

Saturn Girl nodded, glad she had figured it out. The legion had had a space outpost built a couple years back so that they could more easily monitor all the galaxies at once, it was the perfect place to take Brainy. "Yeah, and from there we will figure out where the best place to hide Brainy is. He will have real equipment and be able to build himself anything he needs to hide himself in the world. We are a family Violet, all of us. We can't let Brainy down!"

* * *

 **Present Day**

* * *

"Woah," Brainy grinned at his friends. "So you all are really helping me?"

"Why would you ever doubt it?" Bouncy Boy laughed, punching his friend on the shoulder gently.

"Yeah Brainy, for one with a twelfth level intellect, I am really surprised you didn't expect this to be what was really happening." Saturn Girl laughed smugly and he glanced at her, shrugging apologetically.

"I'm sorry I ever doubted you. I guess I have just started to expect that the whole world is out to get me."

"Well it's not." Timber Wolf growled in his no-nonsense sort of way. "Most of us don't have much family left, so the Legion is all we have. Family watches each other's back."

Looking around himself, Brainy nodded. "I never really had a family, at least I never thought I did. I guess I was wrong."

"Of course you were!" Lightning Lad laughed. "I'm the only one who's always right!"

"In your dreams," Saturn Girl rolled her eyes.

"No, in _your_ dreams."

"Pardon?"

"Baby," He winked at her, "You know you dream about me!"

Saturn Girl spluttered in outrage and the rest of the friends burst out laughing. _Oh yes,_ Brainy thought to himself, looking around at all those he loved. _A family indeed._

* * *

 **Okay, so I know some of u may ship Brainy and Shrinking Violet, sorry not going to happen in this story, lol. I've been shipping him wif someone since I was 8 and if he's getting with anyone, it's going to be her! Haha, try and guess who it is! I'm not telling though, it's going to be a surprise ^_^**

 **None of u will ever guess! MUAHAHAHAHAHA!**


	6. Chapter 6

**Hey guys, I'm really sorry about how long its taking me to update, I had finals all last week and the studying required was... Intense... Oi... Lol**

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"Legion Jet to Tower, come in Tower?" Saturn Girl called through the comm. It wasn't long before they all heard Cosmic Boy's frantic voice.

"Saturn Girl? Is everything alright, what happened?"

"We're having engine trouble, need backup!" Saturn Girl cast her teammates a venomous glance, warning them to be silent as they all started cracking up.

"You know that everyone is deployed... Is the prisoner secure?"

Clenching her fists angrily, she hissed. "Yes, _Brainy_ is in the cell you had fitted for him. And let me just say: lasers? Overkill much!" Brainy stepped up behind her, laying a gently hand on her shoulder to remind her to calm down.

"Sorry Saturn Girl, just a precaution. We don't know what sort of weird Brainiac powers he may have retained."

Mentally forcing herself not to retaliate, she clenched her teeth as she growled, "Awaiting orders, _Sir_."

"Come on! Don't be like that."

"Awaiting orders SIR!" She repeated angrily and she heard him huff over the comm.

"Alright, go to the Space Tower to fix the ship, how long do you think it will take?"

"I don't know, maybe you could send Shrinking Violet to help?"

"Good idea, she will leave within the hour."

"Thank you, Saturn Girl out." Clicking off the comm set, she grinned at her teammates, "It worked. Let's go Bouncy Boy, fire when ready!"

"Aye, aye ma'am!" He saluted his friend playfully and gunned the -perfectly fine- engine.

"You know," Brainy teased. "We have autopilot for that."

"I'm improvising!" He quipped, turning to wink at Brainy and they both burst into laughter, remembering back so many years before on the mission they had found Timber Wolf when they had gotten into a big argument over 'improvisation'.

"Here we are." Saturn Girl cried out not ten minutes later, "Everyone get ready to land."

As soon as they landed, Brainy hopped out, looking around at the Space Tower in awe. "I can't believe you were able to build this without me!" He gasped, running his hand over the smooth metal walls.

"Believe it or not, Brainy," Lightning Lad winked at him teasingly, "But we aren't as stupid as you may think we are."

"That's not what I..."

"We know," Saturn Girl laughed. "But really though, it would have turned out better if you had been here. Let's just say that are computers... Well, they are no COMPUTO."

"Speaking of which, where IS my computer?"

"Back at Legion HQ." Bouncy Boy rubbed his temples, having to fight off a migraine from just thinking of all the trouble that computer had given them recently. "It's been having a temper tantrum ever since you left!"

"Computers don't have tantrums."

"Tell that to it!"

"Bouncy Boy," Brainy turned angry eyes on his friend. "What. Did. You. Do. To. My. Computer?"

"Um... Nothing?" Backing up, Bouncy boy inflated and took off through the halls, bouncing away from the angry Brainy who chased after him.

Laughing, the other Legionnaires followed. It was good to all be together again.

An hour later, the friends were sitting together in the lounge of the Space Tower, talking animatedly and telling Brainy all about all that had happened since he had been gone. Laughing at the obviously embellished stories his friends told him, Brainy smiled at all of them.

"Thanks guys," His smile melted away, suddenly serious. "I mean it, you didn't have to save me, thank you. And I'm sorry for ever doubting you."

"Don't worry about it," Saturn Girl wrapped her arms around him, startled when he leaned into the embrace, he usually hated physical contact. "We're your friends," Her eyes filled with tears as she stroked his blond hair gently, "We will always be there for you when you need us."

"I know." At that moment, alarms went off in the tower.

"What is it? What's happening?" Lightning Lad gasped as Brainy leaped out of Saturn Girl's embrace, racing towards the consul.

Typing away furiously at the keyboard, a static-filled image of Shrinking Violet appeared on screen. "Violet, violet can you read me?"

"Brainy? That you?!" She yelled, her voice bordering on hysteria as she moved her hands over the controls. The cabin of the jet she was in was swiftly filling with smoke and she coughed loudly, trying to wave the smoke away fro her face.

"Yeah, I'm here! What's going on, are you alright?"

On screen, they could see her turn her panicking face towards the sealed metal doors behind her as something rammed into them, denting it. "No, I'm not! Brainy, you've got to get out of here, they're after you! They need you for something, to build something... I don't know what!"

"Violet, you aren't making sense, who?!" Brainy was starting to panic as he saw the girl he had come to love so dearly, the closest thing he had to a sister, start to cry.

"Run Brainy! Run!" She screamed as the doors flew open and the legionnaires stared in shock as they caught a glimpse of the Fatal Five on the screen before the image blinked out and went black.

"Come on!" Brainy started to run towards the doors, "We have to save her!"

"No Brainy!" Saturn Girl exclaimed, holding out a hand to stop him. "You heard her, they are after you!"

"Yeah, but..."

"No buts, we have to..." She trailed off as an explosion ran through the tower, throwing everyone who wasn't flying to the floor. Saturn Girl was the first one to her feet and started running out, "Bouncy Boy," She ordered, "Stay with Brainy! The rest of you, with me!"

"No Saturn Girl!" He protested, running after her. "I can help!"

"Help from in here!" She snapped, racing out of the Tower with the rest of the legionnaires.


	7. Chapter 7

"This stinks Brainy," Bouncy Boy grumbled. "I hate running from a fight!"

Rolling his eyes to himself as he hurried down the hall of Legion HQ, Brainy spoke quietly, trying not to dwell on the fates of his friends. "We didn't exactly have a choice, we had to back down in order to have a chance to fight another day. Now it is up to us to save our teammates. They will never think to look for us here..." Bouncy Boy and Brainy had barely managed to make it out of the Tower before the Fatal Five had broken in. All of their teammates had been captured, and they had no idea what may have become of them..

"How couldn't they? This is our _home_ , this should be the first place they'll look!"

"No, they will never expect it since they would think we would not be so foolish as to return here. Besides, it appears as if they already attacked the Legion Headquarters considering that Cosmic Boy and all the other legionaries are missing now as well. They wouldn't think to come back here if they have already defeated everyone."

"I think your logic is flawed."

"Who here has a twelfth level intelligence? You? I thought not."

"Cocky," Bouncy Boy muttered.

"Besides, we need time to develop a counter attack, and everything I need to save our friends is in my lab here."

"Counter attack?! Brainy, what can WE do?! We are the only ones left! The rest of the Legion... They are all gone."

"Not yet they aren't!" Brainy stepped into the lab, trailed by Bouncy Boy and let his eyes roam over all the half-finished projects he had left behind after leaving the legion. Suddenly, his eyes lit up in anger and he spun towards his friend, "Who touched my experiments?!"

"Um, let's see... I did, Shrinking Violet, Chameleon Boy, Lightning Lad, Timber Wolf, Phantom Girl, Cosmic Boy, Trip..."

"WHAT WAS EVERYONE DOING IN MY STUFF?!" Brainy practically shrieked and Bouncy Boy burst out laughing.

"Get ahold of yourself, Brainy! It's your own fault for leaving it all out like this. We just couldn't help ourselves, we wanted to see what cool stuff you were working on!"

"Why I outa..." Trailing off, I light bulb seemed to go off in Brainy's big head and he ran across the lab, pulling the sheet off of his Time Travel Platform. "That's it!"

"Oh no... I know that you are a level twelve mega-genius, but you are seriously out of your mind!"

"There is no other option, all of our teammates have been captured, in order to save them we must break the laws of time and recruit heroes from the past."

"But messing with history? That's risky... Even for us."

"It's not like this is the first time we've done it or anything, we recruited superman twice."

"Yeah but that was before the United Planets got onto us for messing with history and forced you to dismantle your Time Travel Platform. We don't have the time to properly fix it Brainy. Recruiting Superman is one thing, he virtually can't be killed so there is little danger to throwing off the time stream when we brought him, but now- well..."

"Now my platform has been disabled, I know. We can send it back in time, into the tower of the Justice League in order to grab a few heroes at random."

"But we don't know who it will take, and we could very well get some of the powerless heroes. Having heroes without powers in the 21st century is one thing, but they will never be able to stand up to the villans in this century! And if one of them dies here, that's it, tons of people could end up never even existing, even some of us!"

"I know, but what other choice do we have?"

"We could come up with another option."

"There is no time. Besides, incomplete records from the 21st century indicates that three heroes from the once great Justice League at one point came to the future, my research concludes that that time is now."

"I've done my homework too Brainy, history says that three heroes came to the future bu-"

"But only two ever made it home."

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 **MUAHAHAHAHAHAHA! Hehe, can anyone guess where I got this scene from? (even if I changed it a little...) MY FAV EPISODE EVER! Even if it may have become a bit of a crossover... it still works! ;) can anyone guess who I ship Brainy wif now? I give imaginary Christmas Cookies, so take a guess!**


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